Heat sausage in a large sauce pan (5 quarts or larger), over medium-high heat on stove top. Saute until sausage is cooked through. Use a slotted spoon to remove meat, leaving fat in bottom of pan.

Add all of the chopped onion to pot and cook until softened, about 5 minutes. Once softened, remove from pot and set aside (take ½ cup of the cooked onion and keep this separated to use for filling). Add garlic and cook until fragrant, about 5 minutes.

Then, add Italian stewed tomatoes (do not drain), tomato sauce, tomato paste, red wine, oregano, garlic, thyme, cayenne, salt, and pepper. Stir well.

Cook pasta shells according to package instructions.

In a medium sized bowl, beat egg, then stir in cottage cheese, mozzarella, ricotta, parsley, basil, oregano, thyme, nutmeg, salt, remaining half of sausage and remaining ½ cup cooked onion. Stir until well mixed.

Fill shells with filling (you will use almost all of the shells).

Preheat oven to 350 degrees.

Pour sauce in the bottom of a 9x13 or larger baking dish. Evenly space out stuffed shells in sauce.